2c:null 2d:["$","title",null,{"children":"USM [code][YouTube] | Jonas Almeida | Observable"}] 32:[] 30:{"id":"3186f34fae8b6509","slug":"usm","title":"USM [code][YouTube]","thumbnail":"215dbe3352960c783059b786309a95c47f3504ed14b4c33f1e2d30eabc8aee79","access_level":"public","create_time":"$D2022-01-04T20:14:38.382Z","update_time":"$D2025-07-29T19:30:14.517Z","view_time":null,"first_public_time":"$D2022-01-04T20:14:46.449Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"0f2e596d5bd6ef6e","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":"starter_2024"},"version":688,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null}],"members":[{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null,"role":"editor"},{"type":"individual","id":"2fe10bd213abfed1","login":"jonasalmeida","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/bd90e360f80f2fda3dd6aa9bdda3474b409710441d06e67f9ac936b3660aba05","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"USM [code][YouTube]","cells":[{"id":0,"value":"

USM ^{[code][YouTube]}

\n\n

This notebook relies on version 2 of [Universal Sequence Maps](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017330/) (USM), which was developed to support work on folding alignment, differential mapping and to make the most of ES6 modules to support client and server side computing with the same codebase.

The USM2 library is explored in this notebook and in the accompanying live web application as supplementary material for the manuscript Iterating scale-independent Genomic signatures, from COVID to Cancer.

\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":50,"value":"

Methods

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":69,"value":"

Loading the USM2 library

The usm2.js library can be loaded through regular script tag, as a CommonJS require, or a modern ES6 dynamic module import:

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":75,"value":"Script tag loading, which injects a ```usm``` class function in the global scope\n``` HTML\n\n```\nCommonJS require:\n``` javascript\nusm = require(\"https://usm.github.io/2/usm2.js\")\n```\nES6 module import\n``` javascript\nusm = (await import(\"https://usm.github.io/2/export.js\")).usm2\n```\nHere, we'll use the former:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":80,"value":"//usm = (await import(\"https://usm.github.io/2/export.js\")).usm2\n//usm = (await import(\"http://localhost:8000/usm2/export.js\")).usm2\nusm = require(\"https://usm.github.io/2/usm2.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":82,"value":"Let's map a small oligonucleotide:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":86,"value":"u = new usm(\n \"ATTAGCCAGGTATGGTGATGCATGCCTGTAGTCAGAGCTACTCAGGAGGCTAAGGTGGGAGGATCACCTG\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":627,"value":"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":91,"value":"### Plotting\nThe basic display is a ```.plot``` method that will use a vectorized ```.plotPoints``` or a rasterized ```.plotCanvas``` depending on the length of the sequence. Note that in each case no binning is explicitly performed (beyond what rasterization will do).","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":230,"value":"u.plot()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":99,"value":"md`\nLet's try something bigger, where the rasterized plotCanvas is automatically use. Note also that the full sequence, say the oncogene EGFR, which is ${egfrSeq.seq.length} nucleotides long, can be called directly from a remote location:\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":115,"value":"egfrSeq = usm.resolveSeq(\n \"https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=399923581&db=nuccore&report=fasta&extrafeat=null&conwithfeat=on&hide-cdd=on&retmode=html&withmarkup=on&tool=portal&log$=seqview\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":134,"value":"egfrUSM = new usm(egfrSeq)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":164,"value":"viewof range = Inputs.range([1, 1024], {\n label: \"USM unit size\",\n value: 256,\n format: (x) => Math.round(x)\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":193,"value":"Forward Map","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":117,"value":"egfrUSM.plotCanvas(Math.round(range)) // default direction is \"forward\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":197,"value":"Backward Map","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":189,"value":"egfrUSM.plot(Math.round(range), \"backward\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":381,"value":"#### FCGR\nThe matrix with subquadrant counts can also be extracted independently - and for any bin size - directly from the individual unit coordinates:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":386,"value":"egfrUSM.fcgr(2 * 2 ** 4)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":246,"value":"Small sequences can also be sudied by plotting their individual coordinates in the iterated map with ```.plotPoints```. This also offers the opportunity to see the recursive seeding of the iterated mapping procedure (blue circle marks beginning of the sequence):","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":396,"value":"viewof smallStequenceDirection = Inputs.select([\"forward\", \"backward\"], {\n label: \"Direction\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":399,"value":"viewof smallSequence = Inputs.textarea({\n label: \"Sequence\",\n value:\n \"ATTAGCCAGGTATGGTGATGCATGCCTGTAGTCAGAGCTACTCAGGAGGCTAAGGTGGGAGGATCACCTG\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":404,"value":"smallSequenceMap.plot(300, smallStequenceDirection)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":425,"value":"smallSequenceMap = new usm(smallSequence, \"ACGT\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":541,"value":"usm.plotlyPoints(new usm(\"CCGTCCGGGAACCGGGGGG\", \"ACGT\"), 500)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":444,"value":"abc = new usm(\"ABCDEFGHIJKLMNOPQRSTUVWXYZ\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":508,"value":"uu = require(\"https://usm.github.io/2/usm2.js\")\n//uu = require(\"http://localhost:8000/usm2/usm2.js\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":515,"value":"uu.Plotly","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":598,"value":"require(\"https://cdn.plot.ly/plotly-2.27.0.min.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":614,"value":"seqAbc = new usm(\"ABCDEFGHIJKLMNOPQRSTUVWXYZ\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":622,"value":"## Aminoacids","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":631,"value":"aa = \"ACDEFGHIKLMNPQRSTVWY\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":643,"value":"seq = \"MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIP\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":634,"value":"[aa.length, seq.length]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":665,"value":"First 100 aminoacids of transcribed EGFR protein","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":636,"value":"ua = new usm(seq, aa)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":677,"value":"Object.entries(ua.edges)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"1","titling":"auto"}} 31:"$30:body"